Variant report

Variant	rs7239880
Chromosome Location	chr18:39524523-39524524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10502776	1.00[CEU][hapmap]
rs1142044	1.00[EUR][1000 genomes]
rs11873469	1.00[EUR][1000 genomes]
rs11873602	1.00[EUR][1000 genomes]
rs11874766	1.00[EUR][1000 genomes]
rs11874775	1.00[EUR][1000 genomes]
rs11874814	1.00[EUR][1000 genomes]
rs11874830	1.00[EUR][1000 genomes]
rs11876547	1.00[EUR][1000 genomes]
rs11876578	1.00[EUR][1000 genomes]
rs11877901	1.00[EUR][1000 genomes]
rs1540057	1.00[EUR][1000 genomes]
rs16975441	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16975447	1.00[EUR][1000 genomes]
rs16975463	1.00[EUR][1000 genomes]
rs16975466	1.00[EUR][1000 genomes]
rs16975521	1.00[EUR][1000 genomes]
rs2469471	1.00[EUR][1000 genomes]
rs490578	1.00[EUR][1000 genomes]
rs493100	1.00[EUR][1000 genomes]
rs525369	1.00[EUR][1000 genomes]
rs542870	1.00[EUR][1000 genomes]
rs55655849	1.00[EUR][1000 genomes]
rs563840	1.00[EUR][1000 genomes]
rs56411890	1.00[EUR][1000 genomes]
rs56751463	1.00[EUR][1000 genomes]
rs56979511	1.00[EUR][1000 genomes]
rs57208863	1.00[EUR][1000 genomes]
rs575366	1.00[EUR][1000 genomes]
rs58298297	1.00[EUR][1000 genomes]
rs583163	1.00[EUR][1000 genomes]
rs58390786	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs584022	1.00[EUR][1000 genomes]
rs586797	1.00[EUR][1000 genomes]
rs58881642	1.00[EUR][1000 genomes]
rs591870	1.00[EUR][1000 genomes]
rs593689	1.00[EUR][1000 genomes]
rs606366	1.00[EUR][1000 genomes]
rs608428	1.00[EUR][1000 genomes]
rs616575	1.00[EUR][1000 genomes]
rs633541	1.00[EUR][1000 genomes]
rs635560	1.00[EUR][1000 genomes]
rs640064	1.00[EUR][1000 genomes]
rs640460	1.00[EUR][1000 genomes]
rs643772	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs645148	1.00[EUR][1000 genomes]
rs647084	1.00[EUR][1000 genomes]
rs6507453	1.00[EUR][1000 genomes]
rs6507454	1.00[EUR][1000 genomes]
rs655693	1.00[EUR][1000 genomes]
rs659950	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6650669	1.00[EUR][1000 genomes]
rs669235	1.00[EUR][1000 genomes]
rs670429	1.00[EUR][1000 genomes]
rs674380	1.00[EUR][1000 genomes]
rs684091	1.00[EUR][1000 genomes]
rs7229485	1.00[EUR][1000 genomes]
rs7237185	1.00[EUR][1000 genomes]
rs7237815	1.00[EUR][1000 genomes]
rs7238919	1.00[EUR][1000 genomes]
rs7240066	1.00[EUR][1000 genomes]
rs7241399	1.00[EUR][1000 genomes]
rs7242077	1.00[EUR][1000 genomes]
rs7245131	1.00[EUR][1000 genomes]
rs7343027	1.00[EUR][1000 genomes]
rs73448558	1.00[EUR][1000 genomes]
rs73451096	1.00[EUR][1000 genomes]
rs73452235	1.00[EUR][1000 genomes]
rs73452297	1.00[EUR][1000 genomes]
rs73452300	1.00[EUR][1000 genomes]
rs73453013	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454552	1.00[EUR][1000 genomes]
rs73454573	1.00[EUR][1000 genomes]
rs73454580	1.00[EUR][1000 genomes]
rs73454581	1.00[EUR][1000 genomes]
rs73454593	1.00[EUR][1000 genomes]
rs73454596	1.00[EUR][1000 genomes]
rs73454602	1.00[EUR][1000 genomes]
rs73950814	1.00[EUR][1000 genomes]
rs8084037	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[EUR][1000 genomes]
rs8085708	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8089142	1.00[EUR][1000 genomes]
rs8090403	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8095945	1.00[EUR][1000 genomes]
rs9948650	1.00[EUR][1000 genomes]
rs9965647	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv2268	chr18:39487042-39531721	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7239880	PIR	trans	brain	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39523400-39525000	Weak transcription	GM12878-XiMat	blood
2	chr18:39524200-39524600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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